What is cistrome and where can I find it?
Cistrome is available at http://cistrome.org/ap/. The term ‘cistrome’ refers to the set of cis -acting targets of a trans -acting factor on a genome-wide scale, also known as the in vivo genome-wide location of transcription factors or histone modifications.
What tools does cistrome have for ChIP-seq?
In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/.
How do you analyze cistrome data?
Computational analyses of cistrome data have become increasingly complex and integrative. Investigators often examine the data from many different angles by combining cistrome, epigenome, genomic sequence, and transcriptome analyses. Many algorithms and tools have been published over the years to facilitate such analyses.
How do I import data into cistrome?
Several methods can be used to import data into Cistrome. The ‘Upload File’ function can import a file from the user’s computer or from an HTTP or FTP file server in the same manner as in Galaxy. In most cases, sequencing facilities will manage the low level base calling and read mapping processes.
Can I use cistrome without an account?
This installation of cistrome (Galaxy instance) has been configured such that only users who are logged in may use it. If you don’t already have an account, you may create one . If playback doesn’t begin shortly, try restarting your device.
How does cistrome-go handle Chip-Seq data?
(1) If a ChIP-seq peak file and a differential expression analysis file (upon the TF’s perturbation) are provided, Cistrome-GO will perform an ensemble mode analysis based on the integration of the two types of data ( Figure 1 ).
How does cistrome-go perform functional enrichment analysis?
Cistrome-GO provides two working modes for functional enrichment analysis of genes regulated by TFs in human and mouse.. (1) If a ChIP-seq peak file and a differential expression analysis file (upon the TF’s perturbation) are provided, Cistrome-GO will perform an ensemble mode analysis based on the integration of the two types of data ( Figure 1 ).